Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008693.1 Hibiscus syriacus cultivar Beakdansim tig00111721_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2243253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1761499 original size:19 final size:18
Alignment explanation
Indices: 1761449--1761499 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
1761439 CTCTGACAGA
1761449 AAAATAAATAATAAAAT-
1 AAAATAAATAATAAAATG
**
1761466 AAAATACTTGCAATAAAATG
1 AAAATAAAT--AATAAAATG
1761486 AAATATAAATAATA
1 AAA-ATAAATAATA
1761500 TATAAATACT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 7 0.27
19 12 0.46
20 3 0.12
21 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAATAAATAATAAAATG
Found at i:1763569 original size:3 final size:3
Alignment explanation
Indices: 1763561--1763642 Score: 105
Period size: 3 Copynumber: 28.0 Consensus size: 3
1763551 TTAATATATT
* *
1763561 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1763608 TAA TAA TAA T-A TTA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1763643 ATAAATCAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
2 4 0.06
3 66 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1766001 original size:37 final size:39
Alignment explanation
Indices: 1765911--1766011 Score: 127
Period size: 37 Copynumber: 2.7 Consensus size: 39
1765901 AAAAGAATAA
1765911 GGGGAAAATGATCATTTTTGCAATCATTAGGAGTTAAGT
1 GGGGAAAATGATCATTTTTGCAATCATTAGGAGTTAAGT
* ** ** *
1765950 TGTCATTATG-TCA-TTATGCAATCATTAGGAGTTAAG-
1 GGGGAAAATGATCATTTTTGCAATCATTAGGAGTTAAGT
1765986 GGGGAAAATGATCATTTTTGCAATCA
1 GGGGAAAATGATCATTTTTGCAATCA
1766012 AAGTTATGAT
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
36 5 0.10
37 25 0.52
38 13 0.27
39 5 0.10
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (39 bp):
GGGGAAAATGATCATTTTTGCAATCATTAGGAGTTAAGT
Found at i:1767431 original size:14 final size:15
Alignment explanation
Indices: 1767400--1767436 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1767390 GGAGTGACAA
1767400 AAATATTTAATATAT
1 AAATATTTAATATAT
1767415 AAA-ATTTAAT-TATT
1 AAATATTTAATATA-T
1767429 AAATATTT
1 AAATATTT
1767437 TTTTAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATTTAATATAT
Found at i:1770531 original size:193 final size:193
Alignment explanation
Indices: 1770269--1770672 Score: 458
Period size: 193 Copynumber: 2.1 Consensus size: 193
1770259 TAGTAGTTTT
* * ** * * *
1770269 AATGATGTTTATATATAACGTCACTTTATAATTGATTATTGATGACAACTAGTTACGTTACTAAA
1 AATGATGATTATGTATAACACCACTTTATAATTGATTATTCATGACAACTAGTTAAGTCACTAAA
* *
1770334 TTATATAAAATTTCT-TTATTGATAATTTATATCGTCACAAATAACACATTAAAAT-AATCTTAT
66 TTATATAAAATTT-TGTTATTGATAATTTATATCGCCACAAATAACACATTAAAATCAA-CCTAT
* ** *
1770397 ATGTGGCGAAAGAGATATTGTCACACTTTTAGTGACATAATATAAAT-GTTACCTAATAATATTA
129 ATGTGACGAAAGAGATATTACCACACTTTTAGTAACATAATAT--ATCGTTACCTAATAATATTA
1770461 TG
192 TG
* * * *
1770463 AATGATGCTTATGTATAACACCACTTTATGATTTA-TATTCCATGACAACTTGTTAAGTCACT-A
1 AATGATGATTATGTATAACACCACTTTATAATTGATTATT-CATGACAACTAGTTAAGTCACTAA
** * * *** *
1770526 ATTATATAAGGTTTTGTTATTGATAATTTATATTGCCACGAATAGTGCATTAAAATCCACCTATA
65 ATTATATAAAATTTTGTTATTGATAATTTATATCGCCACAAATAACACATTAAAATCAACCTATA
* ** *
1770591 TGTGACGAAAGAGATATTACCACATTTTTAGTAATGTAATATATCGTTTCCTAATAATATTATG
130 TGTGACGAAAGAGATATTACCACACTTTTAGTAACATAATATATCGTTACCTAATAATATTATG
*
1770655 AATGATGATTATGCATAA
1 AATGATGATTATGTATAA
1770673 TGTCACTTTT
Statistics
Matches: 176, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
191 2 0.01
192 35 0.20
193 91 0.52
194 48 0.27
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (193 bp):
AATGATGATTATGTATAACACCACTTTATAATTGATTATTCATGACAACTAGTTAAGTCACTAAA
TTATATAAAATTTTGTTATTGATAATTTATATCGCCACAAATAACACATTAAAATCAACCTATAT
GTGACGAAAGAGATATTACCACACTTTTAGTAACATAATATATCGTTACCTAATAATATTATG
Found at i:1777608 original size:24 final size:24
Alignment explanation
Indices: 1777564--1777613 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1777554 ATAAAGAACC
*
1777564 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1777588 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
1777612 AA
1 AA
1777614 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1781278 original size:22 final size:22
Alignment explanation
Indices: 1781236--1781279 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1781226 AATCAGATCA
* *
1781236 AAAATTAATTACAAAATAAAAT
1 AAAATAAATTACAAAAAAAAAT
*
1781258 AAAATAAATTAAAGAAAAAAAA
1 AAAATAAATTACA-AAAAAAAA
1781280 ACTTGAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAATAAATTACAAAAAAAAAT
Found at i:1787315 original size:17 final size:16
Alignment explanation
Indices: 1787293--1787326 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1787283 TAAAGACAGT
1787293 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1787310 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1787326 A
1 A
1787327 TCCTCACGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1787845 original size:24 final size:24
Alignment explanation
Indices: 1787801--1787850 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1787791 ATAAAGAACC
*
1787801 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1787825 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
1787849 AA
1 AA
1787851 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1803540 original size:39 final size:39
Alignment explanation
Indices: 1803490--1803571 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
1803480 CACACAAACT
* *
1803490 CATGAACTATTACTTTTGTGGCAAGTCACACACATTTTA
1 CATGAACTATTACCTTTGTGGCAAGCCACACACATTTTA
*
1803529 CATGTACTATTACCTTTGTGGCAAGCCACACACATTTTA
1 CATGAACTATTACCTTTGTGGCAAGCCACACACATTTTA
1803568 CATG
1 CATG
1803572 CAAATGTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (39 bp):
CATGAACTATTACCTTTGTGGCAAGCCACACACATTTTA
Found at i:1809218 original size:5 final size:5
Alignment explanation
Indices: 1809210--1809236 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1809200 ATATGATGAG
1809210 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1809237 TACTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:1809578 original size:21 final size:21
Alignment explanation
Indices: 1809531--1809579 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
1809521 CCTCGTCAAC
1809531 CTTTT-TCTTTTTTTCTCTCT
1 CTTTTCTCTTTTTTTCTCTCT
* *
1809551 CATTTTTCTCTTTTTTTTTCTTT
1 C--TTTTCTCTTTTTTTCTCTCT
1809574 CTTTTC
1 CTTTTC
1809580 CTCCCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
22 4 0.17
23 14 0.58
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (21 bp):
CTTTTCTCTTTTTTTCTCTCT
Found at i:1817578 original size:7 final size:7
Alignment explanation
Indices: 1817566--1817590 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1817556 GTTATTCTTA
1817566 TTTTTCT
1 TTTTTCT
1817573 TTTTTCT
1 TTTTTCT
1817580 TTTTTCT
1 TTTTTCT
1817587 TTTT
1 TTTT
1817591 ATGGTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:1824198 original size:20 final size:19
Alignment explanation
Indices: 1824144--1824200 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
1824134 TTAACATTAA
* *
1824144 GTATCAAAATTAATATTATT
1 GTATCAAAATTAAAATT-TC
* *
1824164 G-ATCAATATTGAAATTTGC
1 GTATCAAAATTAAAATTT-C
1824183 GTATCAAAATTAAAATTT
1 GTATCAAAATTAAAATTT
1824201 AAGATTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 15 0.52
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (19 bp):
GTATCAAAATTAAAATTTC
Found at i:1826122 original size:28 final size:28
Alignment explanation
Indices: 1826079--1826140 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1826069 GCCAACTGAT
*
1826079 CTAACAACCTACACAC-GCTACATAATTG
1 CTAACAACCTACACACATC-ACATAATTG
** *
1826107 CTAACAACCTGTACACATCACTTAATTG
1 CTAACAACCTACACACATCACATAATTG
1826135 CTAACA
1 CTAACA
1826141 TTCACCCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.39, C:0.31, G:0.06, T:0.24
Consensus pattern (28 bp):
CTAACAACCTACACACATCACATAATTG
Found at i:1828496 original size:47 final size:47
Alignment explanation
Indices: 1828427--1828521 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1828417 AAGCTTAATG
1828427 GTTTGTGGATGTTTTTATTATTTTATGCTTTGACTCTATGATTATGT
1 GTTTGTGGATGTTTTTATTATTTTATGCTTTGACTCTATGATTATGT
1828474 GTTTGTGGATGTTTTTATTATTTTATGCTTTGACTCTATGATTATGT
1 GTTTGTGGATGTTTTTATTATTTTATGCTTTGACTCTATGATTATGT
1828521 G
1 G
1828522 CTGTTACACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.17, C:0.06, G:0.20, T:0.57
Consensus pattern (47 bp):
GTTTGTGGATGTTTTTATTATTTTATGCTTTGACTCTATGATTATGT
Found at i:1837462 original size:20 final size:20
Alignment explanation
Indices: 1837417--1837468 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1837407 TGATGTAATT
*
1837417 AGTATCGATACCGAGAGGGA
1 AGTATCGATACCGAGAGGAA
*
1837437 TGTATCGATACCGAGA-GAA
1 AGTATCGATACCGAGAGGAA
1837456 AGATATCGATACC
1 AG-TATCGATACC
1837469 ATTAAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCGAGAGGAA
Found at i:1837559 original size:20 final size:22
Alignment explanation
Indices: 1837510--1837562 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1837500 ACCGTAACAG
1837510 AGTATCGATACCATAGTATAGT
1 AGTATCGATACCATAGTATAGT
* *
1837532 ATTATCGATACCATGGTA-AG-
1 AGTATCGATACCATAGTATAGT
*
1837552 GGTATCGATAC
1 AGTATCGATAC
1837563 TAACGAACCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 9 0.33
21 2 0.07
22 16 0.59
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGT
Found at i:1837964 original size:58 final size:58
Alignment explanation
Indices: 1837891--1838459 Score: 811
Period size: 58 Copynumber: 9.8 Consensus size: 58
1837881 TTCGCACTAA
* * * *
1837891 GTGTGCAAAATGTTAAGAAATTCTTACTAAGTGTATGAGTTTCCGTATTGGGTACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
1837949 GTGTGCAAAAAGTTAAGAAACTCATAAC-AAGTGTATGAATTTTCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCAT-ACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * **
1838007 GTGTGGAGATAGTTAAGAAATTCATACTAAGTGTATGAATTTCTATATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
1838065 GTGTACAAAAAGTTAAAAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * **
1838123 ATGTGCAAAAAGTTAATAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCACATTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC-TTT
*
1838182 -TGTGCAAAAGGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
1838239 GTGTGCAAAAAGTTAAGAAATTCATATTAAGTGTATAAATTTTCGTATTTGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * * *
1838297 GTGTGAAAAAAGTTAAGAAATTCATACTATGTGTATGAATTTACGTAAT-GGAACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
1838354 GTGTACAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACCTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
1838412 GTGTGCTAAAAGTTAAGAGATTCATACTAAGTGTATGAATTTCTGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1838460 GGGAAATATG
Statistics
Matches: 454, Mismatches: 52, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
57 56 0.12
58 393 0.87
59 5 0.01
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:1844582 original size:20 final size:20
Alignment explanation
Indices: 1844557--1844612 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1844547 AATGTAATTA
1844557 GTATCGATACCGAGAGGCAT
1 GTATCGATACCGAGAGGCAT
*
1844577 GTATCGATACCGAGAGGGAT
1 GTATCGATACCGAGAGGCAT
1844597 GTATCGATACCGAGAG
1 GTATCGATACCGAGAG
1844613 AAAGGTATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.32, T:0.20
Consensus pattern (20 bp):
GTATCGATACCGAGAGGCAT
Found at i:1844620 original size:20 final size:20
Alignment explanation
Indices: 1844557--1844627 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1844547 AATGTAATTA
*
1844557 GTATCGATACCGAGAGGCAT
1 GTATCGATACCGAGAGGAAT
*
1844577 GTATCGATACCGAGAGGGAT
1 GTATCGATACCGAGAGGAAT
* *
1844597 GTATCGATACCGAGAGAAAG
1 GTATCGATACCGAGAGGAAT
*
1844617 GTATTGATACC
1 GTATCGATACC
1844628 ATTAAAAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GTATCGATACCGAGAGGAAT
Found at i:1845117 original size:58 final size:58
Alignment explanation
Indices: 1845049--1845555 Score: 809
Period size: 58 Copynumber: 8.8 Consensus size: 58
1845039 ATGGAACAAA
* *
1845049 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATTGGGCGCTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
1845107 GTGTACAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGACACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1845165 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
1845223 ATATG-AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGACACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
1845280 GTGTGCAAAAAGTTAAGAAATTCATACAAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
1845338 ATGTGCAAAACGTTAAAAAATTCATACTAAGTGTATGAATTTCCGTATTGAGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
1845396 ATGTGTAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
1845454 GTGTGTAAAATGTTAAGAAATTCGTACTAAGTTTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
1845512 GTGCGCAAAAAGTTAAGAAATTCTTACTAAGTGTATGAATTTCC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCC
1845556 ACATTAGTAC
Statistics
Matches: 413, Mismatches: 35, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 0.13
58 359 0.87
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:1845345 original size:173 final size:174
Alignment explanation
Indices: 1845055--1845555 Score: 824
Period size: 173 Copynumber: 2.9 Consensus size: 174
1845045 CAAAGTGTGC
* * *
1845055 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTATTGGGCGCTTTGTGTACAAAAAGT
1 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGT
* *
1845120 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGACACTTTGTGTGCAAAAAGTTAAGAAA
66 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAA
*
1845185 TTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTATATG-
131 TTCATACTAAGTGTATGAATTTCCGTATTGAGCACTTTATATGT
*
1845228 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGACACTTTGTGTGCAAAAAGT
1 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGT
* * * *
1845293 TAAGAAATTCATACAAAGTGTATGAATTTCCGTATTGGGCACTTTATGTGCAAAACGTTAAAAAA
66 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAA
*
1845358 TTCATACTAAGTGTATGAATTTCCGTATTGAGCACTTTATGTGT
131 TTCATACTAAGTGTATGAATTTCCGTATTGAGCACTTTATATGT
* * *
1845402 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGTAAAATGT
1 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGT
* * *
1845467 TAAGAAATTCGTACTAAGTTTATGAATTTCCGTATTGGGCACTTTGTGCGCAAAAAGTTAAGAAA
66 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAA
*
1845532 TTCTTACTAAGTGTATGAATTTCC
131 TTCATACTAAGTGTATGAATTTCC
1845556 ACATTAGTAC
Statistics
Matches: 303, Mismatches: 24, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
173 161 0.53
174 142 0.47
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (174 bp):
AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGT
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAAA
TTCATACTAAGTGTATGAATTTCCGTATTGAGCACTTTATATGT
Found at i:1846525 original size:15 final size:15
Alignment explanation
Indices: 1846505--1846538 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1846495 TCCACGATAA
1846505 TTCATATTACCTTTG
1 TTCATATTACCTTTG
1846520 TTCATATTACCTTTG
1 TTCATATTACCTTTG
1846535 TTCA
1 TTCA
1846539 ACATTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (15 bp):
TTCATATTACCTTTG
Found at i:1872421 original size:4 final size:4
Alignment explanation
Indices: 1872412--1872461 Score: 59
Period size: 4 Copynumber: 12.2 Consensus size: 4
1872402 AGGAGATGGT
1872412 AATA AATA AATAA AATA AA-A AATA AA-A ATATA ATATA AATA AATA AATA
1 AATA AATA AAT-A AATA AATA AATA AATA A-ATA A-ATA AATA AATA AATA
1872461 A
1 A
1872462 GAAGAAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 5 0.12
4 26 0.62
5 11 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1872476 original size:25 final size:23
Alignment explanation
Indices: 1872419--1872477 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
1872409 GGTAATAAAT
*
1872419 AAATAAAATAAAAAATAAAAATA
1 AAATAAAATAAAAAATAAAAAGA
* *
1872442 TAATATAAATAAATAAATAAGAAGA
1 AAATA-AAATAAA-AAATAAAAAGA
1872467 AAATGAAAATA
1 AAAT-AAAATA
1872478 TCTTTGACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 4 0.14
24 7 0.24
25 17 0.59
26 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (23 bp):
AAATAAAATAAAAAATAAAAAGA
Found at i:1875331 original size:16 final size:16
Alignment explanation
Indices: 1875301--1875342 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1875291 TTACTGACAT
*
1875301 TTCTTT-GAGAGAAAC
1 TTCTTTCGAGAAAAAC
1875316 TTCTTTCGAGAAAAAC
1 TTCTTTCGAGAAAAAC
*
1875332 TCCTGTTCGAG
1 TTCT-TTCGAG
1875343 CAACAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (16 bp):
TTCTTTCGAGAAAAAC
Found at i:1880704 original size:23 final size:23
Alignment explanation
Indices: 1880678--1880733 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1880668 CCCTTTTGAT
*
1880678 TTTTCATCTTGAACCCTATTTTC
1 TTTTCATCTTGAACCCCATTTTC
1880701 TTTTCATCTTGAACCCCATTTTC
1 TTTTCATCTTGAACCCCATTTTC
1880724 TTTTCATCTT
1 TTTTCATCTT
1880734 TTTTCTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTCATCTTGAACCCCATTTTC
Found at i:1880749 original size:14 final size:15
Alignment explanation
Indices: 1880719--1880756 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1880709 TTGAACCCCA
1880719 TTTTCTTTTCATCTT
1 TTTTCTTTTCATCTT
1880734 TTTTCTTATT-AT-TT
1 TTTTCTT-TTCATCTT
1880748 TTTTCTTTT
1 TTTTCTTTT
1880757 TTGTTCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 9 0.41
15 9 0.41
16 2 0.09
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTCATCTT
Found at i:1884649 original size:24 final size:25
Alignment explanation
Indices: 1884612--1884658 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1884602 ATCATTTTAA
*
1884612 TTACTTATCCATTTT-CATTATATCC
1 TTACTAATCCATTTTAC-TTATATCC
1884637 TTACTAAT-CATTTTACTTATAT
1 TTACTAATCCATTTTACTTATAT
1884659 TTCTTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (25 bp):
TTACTAATCCATTTTACTTATATCC
Found at i:1900421 original size:45 final size:45
Alignment explanation
Indices: 1900372--1900458 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
1900362 TCAAAATAGC
*
1900372 CTGAGTACATCGATGCATGGCT-TGTGCATCGATGCATCAAATCCA
1 CTGAGTACATCGATGCATGG-TATGTGCATCGATGCATAAAATCCA
*
1900417 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAAT
1 CTGAGTACATCGATGCATGGTATGTGCATCGATGCATAAAAT
1900459 GCATTCGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (45 bp):
CTGAGTACATCGATGCATGGTATGTGCATCGATGCATAAAATCCA
Found at i:1900506 original size:20 final size:20
Alignment explanation
Indices: 1900481--1900518 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1900471 CAAAATATTC
1900481 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
* *
1900501 ATTGGTGTATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1900519 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:1902691 original size:20 final size:20
Alignment explanation
Indices: 1902666--1902717 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1902656 ACCAGACGGA
*
1902666 TGCATCGATGCATGGTAGTG
1 TGCATCGATGCATGGCAGTG
1902686 TGCATCGATGCATGGCAGTG
1 TGCATCGATGCATGGCAGTG
1902706 TGCATCGATGCA
1 TGCATCGATGCA
1902718 CAGTCAAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCATGGCAGTG
Found at i:1904819 original size:38 final size:37
Alignment explanation
Indices: 1904777--1904852 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 37
1904767 CACTCACTTC
*
1904777 GATAACAAATCAATTGCTAAGGCATTGAAGAAATATAG
1 GATAACAAAGCAATTGCTAAGGCATTGAAGAAA-ATAG
1904815 GATAACAAAGCAATTGCTAAGGCATTGAAGAAAATAG
1 GATAACAAAGCAATTGCTAAGGCATTGAAGAAAATAG
1904852 G
1 G
1904853 GTGCGTCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (37 bp):
GATAACAAAGCAATTGCTAAGGCATTGAAGAAAATAG
Found at i:1916589 original size:2 final size:2
Alignment explanation
Indices: 1916578--1916606 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1916568 TAAAGGTAAT
1916578 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1916607 CAAATAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1918721 original size:213 final size:216
Alignment explanation
Indices: 1918350--1918761 Score: 632
Period size: 213 Copynumber: 1.9 Consensus size: 216
1918340 TAAGACCTAC
* * * * *
1918350 GGGTAGGATGTTTTCACATGATTTTTAAAATATGAGAAAGTGATTTTCAAGGTTTCTCATTTTGT
1 GGGTAGGATGTCTTCACATGA-TTTTAAAATATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGT
* * *
1918415 ATTTTCAGAAAATGAATTTTTTGAAAAATAAGAAAACGATTTCCAAAGTTTCTTACACAGTAGAC
65 ATTTTCAGAAAATGAAATTTTTGAAAAATAAGAAAACGATTTCCAAAGTCTCTTACACAGTAAAC
* *
1918480 TATTTCCAAAATCGGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCACGATGATTAAATCCT
130 TATTTCCAAAATCGGTAAGTCATTCGGGCCATCAATAAGCCTTTCGAGCACGATGATTAAATCCT
1918545 TCGGGCTATCTATATGACCTTT
195 TCGGGCTATCTATATGACCTTT
1918567 GGGTAGGATGTCTTCACATGA-TTT-AAA-ATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA
1 GGGTAGGATGTCTTCACATGATTTTAAAATATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA
* * * * *
1918629 TTTTCAGAAGATGAAATTTTTGAAAAGTAAGAAAGCGATTTTCAAAGTCTCTTACCCAGTAAACT
66 TTTTCAGAAAATGAAATTTTTGAAAAATAAGAAAACGATTTCCAAAGTCTCTTACACAGTAAACT
* * *
1918694 ATTTTCAAAATCGGTAAGTCCTTCGGGCCATCAATAAGCCTTTCGAGCATGATGATTAAATCCTT
131 ATTTCCAAAATCGGTAAGTCATTCGGGCCATCAATAAGCCTTTCGAGCACGATGATTAAATCCTT
1918759 CGG
196 CGG
1918762 CTCATCTGTC
Statistics
Matches: 177, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
213 151 0.85
214 3 0.02
215 3 0.02
217 20 0.11
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (216 bp):
GGGTAGGATGTCTTCACATGATTTTAAAATATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA
TTTTCAGAAAATGAAATTTTTGAAAAATAAGAAAACGATTTCCAAAGTCTCTTACACAGTAAACT
ATTTCCAAAATCGGTAAGTCATTCGGGCCATCAATAAGCCTTTCGAGCACGATGATTAAATCCTT
CGGGCTATCTATATGACCTTT
Found at i:1918811 original size:41 final size:42
Alignment explanation
Indices: 1918733--1918811 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
1918723 ATCAATAAGC
1918733 CTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGG
1 CTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGG
* * *
1918775 CTTTCGAGACA-GATGA-TAAGTCCTTTGGGTCATCTGT
1 CTTTCGAG-CATGATGATTAAATCCTTCGGCTCATCTGT
1918812 AAGACCTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 18 0.55
42 13 0.39
43 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (42 bp):
CTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGG
Found at i:1919093 original size:259 final size:260
Alignment explanation
Indices: 1918591--1919099 Score: 761
Period size: 259 Copynumber: 2.0 Consensus size: 260
1918581 CACATGATTT
* * * *
1918591 AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAGATGAAATTTTTGAAAAG
1 AAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
* * * *
1918656 TAAGAAAGCGATTTTCAAAGTCTCTTACCCAGTAAACTATTTTCAAAATCGGTAAGTCCTTCGGG
66 TAAGAAAGCGATTTCCAAACTCTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
* *
1918721 CCATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGACA
131 CCATCAATAAGCCTTTCGAGCATGAGGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGAAA
* * * *
1918786 GATGATAAGTCCTTTGGGTCATCTGTAAGACCTTTGGGCAAGATGCTTTCATATGATGTTTGTGA
196 GATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCATATGATGTTTGTGA
*
1918851 AAAATGAGAAAGTGATTTCCAAAGTTTAT-ATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
1 AAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
* *
1918915 TAAGAAAGTGATTTCCAAACTTTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
66 TAAGAAAGCGATTTCCAAACTCTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
* ** * * * * *
1918980 CCGTCCGTAAGTCTTTCGAGCATGAGGATTAAATCCTTCGGGTCATCTGTTAGTCTTTTGA-ATA
131 CCATCAATAAGCCTTTCGAGCATGAGGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGA-A
*
1919044 AGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAATATGCTTTCATATG
195 AGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCATATG
1919100 GTATTTGTAA
Statistics
Matches: 222, Mismatches: 26, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
258 1 0.00
259 194 0.87
260 27 0.12
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (260 bp):
AAAATGAGAAAGCGATTTCCAAAGTTTATCATTTAGTATTTTCAAAAAATGAAATTTTTAAAAAG
TAAGAAAGCGATTTCCAAACTCTCTTACCCAGTAAACTATTTCCAAAATCGATAAGTCCTTCGGG
CCATCAATAAGCCTTTCGAGCATGAGGATTAAATCCTTCGGCTCATCTGTCAGGCTTTCGAGAAA
GATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGAGCAAGATGCTTTCATATGATGTTTGTGA
Found at i:1919618 original size:45 final size:45
Alignment explanation
Indices: 1919446--1919922 Score: 471
Period size: 45 Copynumber: 10.6 Consensus size: 45
1919436 ATAGATTGAT
*
1919446 AGAGGAGTCAATCTTTTAGTGTTGTC-TTCCTTGAATTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT-CTTGACTTTCTCATGA
* * * * *
1919491 AAATGAGTCAGTC-TTTAGTGTTGTCATTCTTGACTTACTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* *
1919535 AGAGGAGTCAATC-TTTAATATTGTCATTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* * * *
1919579 AGAGGAGTCGATCTTTTAGTATTGTCATTCTTGATTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* * * *
1919624 AGA-GAATCCAATCATTTAGTGTTGTCATTCTTGACTTTTTCGTGA
1 AGAGGAGT-CAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* * ** * * *
1919669 AGAGAAATTGATCTTTTAGTGTTTTCATTCTTGAGTTTCTCGTGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* * * * ** *
1919714 AGAGAAGTCGACCTTTTAGTGTTGTGATTCTTGACTTTCTCGCGG
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* * * *
1919759 AGAGGAGTCAACCTTTTAATGATGTTATTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* * * *
1919804 AGAGAAGTCAATCTTTTTGTGTTGTCCTTCTTCACTTTCT-A-GCAA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATG--A
* * *
1919849 ATATGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATGA
1 AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
* * * *
1919894 AGAGGAGTAAACCTTTTATTGATGTCATT
1 AGAGGAGTCAATCTTTTAGTGTTGTCATT
1919923 TAAACTTGAT
Statistics
Matches: 358, Mismatches: 66, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.00
44 78 0.22
45 274 0.77
46 4 0.01
47 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (45 bp):
AGAGGAGTCAATCTTTTAGTGTTGTCATTCTTGACTTTCTCATGA
Found at i:1932610 original size:6 final size:6
Alignment explanation
Indices: 1932569--1932616 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
1932559 ATGTTTAATT
* * *
1932569 AATAAT AATAATA AAT-AA AATAAA AATAGA ACTAAA AATAAA AATAAA
1 AATAAA AATAA-A AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1932617 TATATCTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 4 0.11
6 28 0.80
7 3 0.09
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (6 bp):
AATAAA
Found at i:1950688 original size:17 final size:17
Alignment explanation
Indices: 1950668--1950713 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1950658 TATTTTAATC
* *
1950668 AATGAACTACTTAGTTA
1 AATGAACTACATAGCTA
* *
1950685 AATGAAGTGCATAGCTA
1 AATGAACTACATAGCTA
1950702 AATGAACTACAT
1 AATGAACTACAT
1950714 GTTTAAATGC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (17 bp):
AATGAACTACATAGCTA
Found at i:1953263 original size:48 final size:49
Alignment explanation
Indices: 1953211--1953372 Score: 136
Period size: 48 Copynumber: 3.4 Consensus size: 49
1953201 AAAAAACTCA
* *
1953211 GATGATTTTCTCCACCATCTCTT-TGTGGAGATTAAATCTTGAAACTTT
1 GATGATTTACTCCACCATCTCTTCTGTGGAGATCAAATCTTGAAACTTT
* * * *
1953259 GATGATTTAATCCACCATTTCTTCT-TGGATATCAAAT-TTGGAATCTTT
1 GATGATTTACTCCACCATCTCTTCTGTGGAGATCAAATCTT-GAAACTTT
* * * * * * * * *
1953307 AATGATTTTCTCCA--TTGTCTTGTGGTGAAGATCAAATCTAGACATTTT
1 GATGATTTACTCCACCATCTCTTCT-GTGGAGATCAAATCTTGAAACTTT
1953355 GATGATTTACTCCACCAT
1 GATGATTTACTCCACCAT
1953373 TCCATTGTGA
Statistics
Matches: 86, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
46 6 0.07
47 2 0.02
48 75 0.87
49 2 0.02
50 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (49 bp):
GATGATTTACTCCACCATCTCTTCTGTGGAGATCAAATCTTGAAACTTT
Found at i:1953470 original size:47 final size:46
Alignment explanation
Indices: 1953419--1953573 Score: 125
Period size: 47 Copynumber: 3.3 Consensus size: 46
1953409 TTTCTCTATG
*
1953419 GTCTCTTCATGAATATCAAATATAGAAAGATGATGATTAGCTTCATT
1 GTCTCTTCATGAATATCAAATATAGAAAGATGATGATTA-ATTCATT
* * * * * **
1953466 GTCTCTTCACGAATAAT-GAATCTA-AAAAATTGATGATTTATTTCACC
1 GTCTCTTCATGAAT-ATCAAATATAGAAAGA-TGATGA-TTAATTCATT
* * * * * *
1953513 ATCTTTTTATGAATATCAAATATGGAGAGATGTTGATTCAATTCATT
1 GTCTCTTCATGAATATCAAATATAGAAAGATGATGATT-AATTCATT
1953560 GTCTCTTCATGAAT
1 GTCTCTTCATGAAT
1953574 GATGAGTCTA
Statistics
Matches: 79, Mismatches: 23, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
46 8 0.10
47 63 0.80
48 8 0.10
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (46 bp):
GTCTCTTCATGAATATCAAATATAGAAAGATGATGATTAATTCATT
Found at i:1961791 original size:11 final size:11
Alignment explanation
Indices: 1961775--1961799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1961765 AATACAAAAA
1961775 GAAGTGCAAGT
1 GAAGTGCAAGT
1961786 GAAGTGCAAGT
1 GAAGTGCAAGT
1961797 GAA
1 GAA
1961800 AGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:1961844 original size:23 final size:23
Alignment explanation
Indices: 1961816--1961868 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1961806 AAAATCAGCA
1961816 AAGAAATTGAAGCACTTC-AAAAG
1 AAGAAATTGAAGCAC-TCAAAAAG
**
1961839 AAGAAAATTTCAGCACTCAAAAAG
1 AAG-AAATTGAAGCACTCAAAAAG
1961863 AAGAAA
1 AAGAAA
1961869 AGAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.57, C:0.13, G:0.15, T:0.15
Consensus pattern (23 bp):
AAGAAATTGAAGCACTCAAAAAG
Found at i:1969409 original size:11 final size:13
Alignment explanation
Indices: 1969377--1969406 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1969367 TAGCCAAAGA
1969377 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1969390 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1969402 TGAAA
1 TGAAA
1969407 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1970965 original size:28 final size:28
Alignment explanation
Indices: 1970925--1970979 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1970915 AGAAGAGAAC
1970925 AAAAGGGGTTACTTACACAAGTCACTTT
1 AAAAGGGGTTACTTACACAAGTCACTTT
1970953 AAAAGGGGTTACTTACACAAGTCACTT
1 AAAAGGGGTTACTTACACAAGTCACTT
1970980 CACAACCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (28 bp):
AAAAGGGGTTACTTACACAAGTCACTTT
Found at i:1984434 original size:61 final size:59
Alignment explanation
Indices: 1984321--1984434 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
1984311 CTTATATACA
* *
1984321 TATAGTTTGGGATAAAATTGGAATGTTAAGAAATTTTGGGACTAATTTAGAATGAAAGT
1 TATAGTTTGGGATAAAATTGAAATGTTAAGAAAGTTTGGGACTAATTTAGAATGAAAGT
* * *
1984380 TATAGTTTGGGGATGATATTGAAATGTTCAA-AAAGTTTGAGGATTAATTTAGAAT
1 TATAGTTT-GGGATAAAATTGAAATGTT-AAGAAAGTTTG-GGACTAATTTAGAAT
1984435 CCTATTCATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 8 0.17
60 23 0.49
61 16 0.34
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (59 bp):
TATAGTTTGGGATAAAATTGAAATGTTAAGAAAGTTTGGGACTAATTTAGAATGAAAGT
Found at i:1984446 original size:61 final size:59
Alignment explanation
Indices: 1984321--1984470 Score: 151
Period size: 61 Copynumber: 2.5 Consensus size: 59
1984311 CTTATATACA
* * * *
1984321 TATAGTTTGGGATAAAATTGGAATGTTAAGAAATTTTGGGACTAATTTAGAATGAAAGT
1 TATAGTTTGGGATGAAATTGAAATGTTAAGAAAGTTTGGGACTAATTTAGAATCAAAGT
* * **
1984380 TATAGTTTGGGGATGATATTGAAATGTTCAA-AAAGTTTGAGGATTAATTTAGAATCCTA-T
1 TATAGTTT-GGGATGAAATTGAAATGTT-AAGAAAGTTTG-GGACTAATTTAGAATCAAAGT
* *
1984440 TCATAGTTTAGGGATGAAATTTAAATATTAA
1 T-ATAGTTT-GGGATGAAATTGAAATGTTAA
1984471 AATATTTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
59 8 0.11
60 27 0.36
61 40 0.53
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.37
Consensus pattern (59 bp):
TATAGTTTGGGATGAAATTGAAATGTTAAGAAAGTTTGGGACTAATTTAGAATCAAAGT
Found at i:1985881 original size:23 final size:21
Alignment explanation
Indices: 1985846--1985891 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
1985836 ATTTGTACAC
*
1985846 TTTTTTTGGCATTTCATTAATTA
1 TTTTTATGGCATTT-ATT-ATTA
*
1985869 TTTTTATGTCATTTATTATTA
1 TTTTTATGGCATTTATTATTA
1985890 TT
1 TT
1985892 GCATTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTATGGCATTTATTATTA
Found at i:1989424 original size:23 final size:24
Alignment explanation
Indices: 1989398--1989443 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1989388 AAACACAATA
* *
1989398 ATTT-GAAAATTAACATTTTTTTT
1 ATTTCGAAAATTAAAAATTTTTTT
1989421 ATTTCGAAAATTAAAAATTTTTT
1 ATTTCGAAAATTAAAAATTTTTT
1989444 GGAAAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTCGAAAATTAAAAATTTTTTT
Found at i:1989837 original size:21 final size:21
Alignment explanation
Indices: 1989811--1989851 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1989801 CAGAACCCCA
* *
1989811 GGGGGGTATCGATTCCCCTTT
1 GGGGGGAATCGATTACCCTTT
*
1989832 GGGGGGAATCGGTTACCCTT
1 GGGGGGAATCGATTACCCTT
1989852 CAAAGGGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.22, G:0.37, T:0.29
Consensus pattern (21 bp):
GGGGGGAATCGATTACCCTTT
Found at i:1993660 original size:21 final size:22
Alignment explanation
Indices: 1993636--1993678 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1993626 GAGTTTGTTT
1993636 TCATTTTTCA-ATTTT-GAAACA
1 TCATTTTT-ATATTTTAGAAACA
1993657 TCATTTTTATATTTTAGAAACA
1 TCATTTTTATATTTTAGAAACA
1993679 ATTTCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (22 bp):
TCATTTTTATATTTTAGAAACA
Found at i:1997537 original size:18 final size:17
Alignment explanation
Indices: 1997488--1997543 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
1997478 TTGATAAATT
*
1997488 AACTAGTTTAATGAATG
1 AACTAGTTTAATCAATG
1997505 AACTAGTTTAATCAATG
1 AACTAGTTTAATCAATG
* *
1997522 AACTAATTTTATTCAATG
1 AACT-AGTTTAATCAATG
1997540 AACT
1 AACT
1997544 TGCTTACTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (17 bp):
AACTAGTTTAATCAATG
Found at i:2005927 original size:11 final size:12
Alignment explanation
Indices: 2005911--2005940 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2005901 ACTTCAGTTA
2005911 TTATTTTATT-T
1 TTATTTTATTCT
2005922 TTATTTTATTCT
1 TTATTTTATTCT
2005934 TTATTTT
1 TTATTTT
2005941 TGTTAGGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (12 bp):
TTATTTTATTCT
Found at i:2007943 original size:19 final size:21
Alignment explanation
Indices: 2007919--2007971 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2007909 TTGAGAATAG
2007919 GTATCGATACTGAA-GTAT-A
1 GTATCGATACTGAATGTATAA
2007938 GTATCGATACCAT-AATGTATAA
1 GTATCGATA-C-TGAATGTATAA
2007960 GTATCGATACTG
1 GTATCGATACTG
2007972 GACCTTGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 9 0.31
20 4 0.14
21 6 0.21
22 10 0.34
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
GTATCGATACTGAATGTATAA
Found at i:2008480 original size:15 final size:17
Alignment explanation
Indices: 2008444--2008498 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 17
2008434 TAACCATAAT
* *
2008444 CTATGTGCTTATATG-T
1 CTATGTGATTATATGAA
2008460 CTATGTGA-TAT-TGAA
1 CTATGTGATTATATGAA
2008475 CTATGTGATTATATGAA
1 CTATGTGATTATATGAA
2008492 -TATGTGA
1 CTATGTGA
2008499 AATGTGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 17 0.50
17 4 0.12
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (17 bp):
CTATGTGATTATATGAA
Found at i:2008737 original size:24 final size:24
Alignment explanation
Indices: 2008689--2008737 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2008679 ACATTTCTAT
* *
2008689 GTGGCACTTCAGTGCATATTCTAC
1 GTGGCACTTCAGTCCATATTATAC
2008713 GTGGCACTTCAGTCCA-ATTTATAC
1 GTGGCACTTCAGTCCATA-TTATAC
2008737 G
1 G
2008738 AGTTGTGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (24 bp):
GTGGCACTTCAGTCCATATTATAC
Found at i:2013120 original size:23 final size:24
Alignment explanation
Indices: 2013087--2013154 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
2013077 TTGAGGGTTT
* *
2013087 TACGTGATCCTTCGGGATAA-TTC
1 TACGTGGTCCTTCGGGACAATTTC
2013110 TACGTGGTCCTTCGGGACAATTTC
1 TACGTGGTCCTTCGGGACAATTTC
* *
2013134 TACGCGGTCCTTCAGGACAAT
1 TACGTGGTCCTTCGGGACAAT
2013155 ACTATGAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 18 0.45
24 22 0.55
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (24 bp):
TACGTGGTCCTTCGGGACAATTTC
Found at i:2013255 original size:24 final size:24
Alignment explanation
Indices: 2013187--2013246 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
2013177 TTCTATGTGG
2013187 CACTTCGGTGCATATTCTACGCGT
1 CACTTCGGTGCATATTCTACGCGT
2013211 CACTTCGGTGCATATTCTACGCGT
1 CACTTCGGTGCATATTCTACGCGT
*
2013235 CATTTCGGTGCA
1 CACTTCGGTGCA
2013247 ATTTATACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (24 bp):
CACTTCGGTGCATATTCTACGCGT
Found at i:2015137 original size:21 final size:21
Alignment explanation
Indices: 2015106--2015186 Score: 117
Period size: 21 Copynumber: 3.9 Consensus size: 21
2015096 CAGAGACATT
*
2015106 TACCAAAGTACTTCATCTACA
1 TACCAAGGTACTTCATCTACA
*
2015127 TACCGAGGTACTTCATCTACA
1 TACCAAGGTACTTCATCTACA
* *
2015148 CACCAAGGTACTTCATATACA
1 TACCAAGGTACTTCATCTACA
*
2015169 TACCAATGTACTTCATCT
1 TACCAAGGTACTTCATCT
2015187 TCTTCCATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (21 bp):
TACCAAGGTACTTCATCTACA
Found at i:2016099 original size:13 final size:13
Alignment explanation
Indices: 2016081--2016105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2016071 ACACTTGAAG
2016081 AAAACATAGTAGA
1 AAAACATAGTAGA
2016094 AAAACATAGTAG
1 AAAACATAGTAG
2016106 CATATACATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (13 bp):
AAAACATAGTAGA
Found at i:2019787 original size:18 final size:17
Alignment explanation
Indices: 2019754--2019796 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2019744 TTTACATTCC
* *
2019754 TATAATTTTATTAAAAT
1 TATAATTTAATAAAAAT
2019771 ATATAATTTAATAAAAAT
1 -TATAATTTAATAAAAAT
2019789 TA-AATTTA
1 TATAATTTA
2019797 TTTTTTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAATTTAATAAAAAT
Found at i:2019910 original size:18 final size:17
Alignment explanation
Indices: 2019887--2019933 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
2019877 TGTTTCTGAG
2019887 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGT-AA
* *
2019905 GGAATTGAAATATGTCA
1 GGAATTGAAATCTGTAA
*
2019922 GGAATTGGAATC
1 GGAATTGAAATC
2019934 CAATTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (17 bp):
GGAATTGAAATCTGTAA
Found at i:2019926 original size:17 final size:18
Alignment explanation
Indices: 2019887--2019928 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2019877 TGTTTCTGAG
*
2019887 GGAATTGAAATCTGTGAA
1 GGAATTGAAATATGTGAA
*
2019905 GGAATTGAAATATGT-CA
1 GGAATTGAAATATGTGAA
2019922 GGAATTG
1 GGAATTG
2019929 GAATCCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.38, C:0.05, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGAAATATGTGAA
Found at i:2027077 original size:21 final size:21
Alignment explanation
Indices: 2027053--2027153 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
2027043 GCATGACAAT
*
2027053 GTTAAGTCTTTTTATCAAAAG
1 GTTAAGTCTTTTCATCAAAAG
* *
2027074 GTTAAGTCCTTTCATTGAAAAAG
1 GTTAAGTCTTTTCA-T-CAAAAG
* * * * *
2027097 ATTAAATATTTTCATGAAAAA
1 GTTAAGTCTTTTCATCAAAAG
*
2027118 GTTAAG-CTTTTTTATCAAAAG
1 GTTAAGTC-TTTTCATCAAAAG
* *
2027139 GTTATGTCCTTTCAT
1 GTTAAGTCTTTTCAT
2027154 TGAAAGGTCT
Statistics
Matches: 58, Mismatches: 18, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
21 40 0.69
22 3 0.05
23 15 0.26
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (21 bp):
GTTAAGTCTTTTCATCAAAAG
Found at i:2027101 original size:23 final size:21
Alignment explanation
Indices: 2027033--2027123 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 21
2027023 CATGAGAAGA
* *
2027033 TTAAGTA-TTTGCATGACAATG
1 TTAAGTACTTT-CATGAAAAAG
* * *
2027054 TTAAGT-CTTTTTATCAAAAGG
1 TTAAGTAC-TTTCATGAAAAAG
*
2027075 TTAAGTCCTTTCATTGAAAAAG
1 TTAAGTACTTTCA-TGAAAAAG
* *
2027097 ATTAAATATTTTCATGAAAAAG
1 -TTAAGTACTTTCATGAAAAAG
2027119 TTAAG
1 TTAAG
2027124 CTTTTTTATC
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
21 26 0.48
22 18 0.33
23 10 0.19
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
TTAAGTACTTTCATGAAAAAG
Found at i:2027133 original size:65 final size:65
Alignment explanation
Indices: 2027029--2027158 Score: 199
Period size: 65 Copynumber: 2.0 Consensus size: 65
2027019 TCTTCATGAG
* * *
2027029 AAGATTAAGTATTTGCATGACAATGTTAAGTCTTTTTATCAAAAGGTTAAGTCCTTTCATTGAAA
1 AAGATTAAATATTTGCATGAAAAAGTTAAGTCTTTTTATCAAAAGGTTAAGTCCTTTCATTGAAA
* *
2027094 AAGATTAAATATTTTCATGAAAAAGTTAAG-CTTTTTTATCAAAAGGTTATGTCCTTTCATTGAA
1 AAGATTAAATATTTGCATGAAAAAGTTAAGTC-TTTTTATCAAAAGGTTAAGTCCTTTCATTGAA
2027158 A
65 A
2027159 GGTCTTAACC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 1 0.02
65 58 0.98
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (65 bp):
AAGATTAAATATTTGCATGAAAAAGTTAAGTCTTTTTATCAAAAGGTTAAGTCCTTTCATTGAAA
Found at i:2027278 original size:15 final size:15
Alignment explanation
Indices: 2027234--2027278 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2027224 CAGATTTGAA
* *
2027234 TTCCTTTCAATTTAC
1 TTCCTTTCAATTCAT
2027249 TTCCTTTCGAA-TCAT
1 TTCCTTTC-AATTCAT
2027264 TTCCTTTCAATTCAT
1 TTCCTTTCAATTCAT
2027279 CAAATTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.20, C:0.27, G:0.02, T:0.51
Consensus pattern (15 bp):
TTCCTTTCAATTCAT
Found at i:2034719 original size:2 final size:2
Alignment explanation
Indices: 2034712--2034766 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
2034702 ATTACTCATT
*
2034712 TA TA TA TA TA -A CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2034753 TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA T
2034767 TAAATACACA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2054885 original size:187 final size:187
Alignment explanation
Indices: 2054561--2054929 Score: 585
Period size: 187 Copynumber: 2.0 Consensus size: 187
2054551 GATAGTAATG
* * * *
2054561 ATGTTCACTATCATTCTACTGTTTAGTCTAATAAGATGATGTATTGGTACAATAGGAAGTGCCAA
1 ATGTTAACCATCATTCTACTGTTTAGTCTAACAAGATGATGTATTGGCACAATAGGAAGTGCCAA
* *
2054626 TGTTGGATTAAGGAAAACCCTCATTCATGCATAAGTATAGTATGGATTAAAGAAATGTTTTGAAT
66 TGTTGGATTAAGAAAAACCCTCATTCATGCACAAGTATAGTATGGATTAAAGAAATGTTTTGAAT
* * * *
2054691 TTCTGATGTGCCATTTGTAACTCGTATTGATTCATGTATACGAGTTATGTGTGTTAC
131 TTCTGATGTGACATCTATAACTCGTATTGATTCACGTATACGAGTTATGTGTGTTAC
* * *
2054748 ATGTTAACCATCATTCTATTGTTTTGTCTAACAAGATGATGTATTGGCACAATAGGAAGTGTCAA
1 ATGTTAACCATCATTCTACTGTTTAGTCTAACAAGATGATGTATTGGCACAATAGGAAGTGCCAA
* * *
2054813 TGTTGGATTAATAAAAACCCTCGTTCATGCACAAGTATAGTATGGATTAAATAAATGTTTTGAAT
66 TGTTGGATTAAGAAAAACCCTCATTCATGCACAAGTATAGTATGGATTAAAGAAATGTTTTGAAT
*
2054878 TTCTGATGTGACATCTATAACTCGTATTGATTCACGTATATGAGTTATGTGT
131 TTCTGATGTGACATCTATAACTCGTATTGATTCACGTATACGAGTTATGTGT
2054930 ATACTAGTTA
Statistics
Matches: 165, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
187 165 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (187 bp):
ATGTTAACCATCATTCTACTGTTTAGTCTAACAAGATGATGTATTGGCACAATAGGAAGTGCCAA
TGTTGGATTAAGAAAAACCCTCATTCATGCACAAGTATAGTATGGATTAAAGAAATGTTTTGAAT
TTCTGATGTGACATCTATAACTCGTATTGATTCACGTATACGAGTTATGTGTGTTAC
Found at i:2058388 original size:43 final size:43
Alignment explanation
Indices: 2058335--2058431 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
2058325 CCATATTACG
* * * *
2058335 CTGATTCAACT-CATTCTATGAAGAATCAAGCAAAAGTTTTTCA
1 CTGATCCAACTCCA-TCTATAAAGAATCAAGCAAAAGGTTGTCA
* * **
2058378 CTGATCCAACTCCATCTGTAAAGGATCAAGTGAAAGGTTGTCA
1 CTGATCCAACTCCATCTATAAAGAATCAAGCAAAAGGTTGTCA
2058421 CTGATCCAACT
1 CTGATCCAACT
2058432 ACTTCTGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
43 43 0.96
44 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (43 bp):
CTGATCCAACTCCATCTATAAAGAATCAAGCAAAAGGTTGTCA
Found at i:2058616 original size:43 final size:43
Alignment explanation
Indices: 2058568--2058716 Score: 111
Period size: 43 Copynumber: 3.4 Consensus size: 43
2058558 ATTTCTTTTG
* * *
2058568 TGAAGAGCCGAACAAAATGACATTGTTGATCCAACTCCTTCTA
1 TGAAGAACCAAACAAAATGACAATGTTGATCCAACTCCTTCTA
** * * *
2058611 TGAAGAATTAAACAAAATGTCAATGTTGATCTACCTCCTTCTA
1 TGAAGAACCAAACAAAATGACAATGTTGATCCAACTCCTTCTA
* * * ** * *
2058654 TGATAAAATCGAGAAAAATAAT-ATTATGCTGATCCAACTCCTTCTG
1 TGA-AGAA-CCA-AACAA-AATGACAATGTTGATCCAACTCCTTCTA
*
2058700 TGAAGAATCAAACAAAA
1 TGAAGAACCAAACAAAA
2058717 GATTGGTACT
Statistics
Matches: 79, Mismatches: 23, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
42 2 0.03
43 42 0.53
44 4 0.05
45 4 0.05
46 24 0.30
47 3 0.04
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (43 bp):
TGAAGAACCAAACAAAATGACAATGTTGATCCAACTCCTTCTA
Found at i:2069189 original size:52 final size:52
Alignment explanation
Indices: 2069127--2069249 Score: 210
Period size: 52 Copynumber: 2.4 Consensus size: 52
2069117 ATAAAAAACG
2069127 ATCTCTCGATGCTCTTACAATCCCAAGACATGATTCACCAAGACCCCAGGCA
1 ATCTCTCGATGCTCTTACAATCCCAAGACATGATTCACCAAGACCCCAGGCA
* *
2069179 ATCTCTCGATGCTCTTACATTGCCAAGACATGATTCACCAAGACCCCAGGCA
1 ATCTCTCGATGCTCTTACAATCCCAAGACATGATTCACCAAGACCCCAGGCA
* *
2069231 ATCTTTCGAAGCTCTTACA
1 ATCTCTCGATGCTCTTACA
2069250 GTATCAAGGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (52 bp):
ATCTCTCGATGCTCTTACAATCCCAAGACATGATTCACCAAGACCCCAGGCA
Found at i:2084017 original size:433 final size:433
Alignment explanation
Indices: 2083211--2084073 Score: 1631
Period size: 433 Copynumber: 2.0 Consensus size: 433
2083201 TCAAAATTTA
*
2083211 CATTTTGTTTACTAGTCAAAATTTGGGATATCACAAAGGAAAATATAAAAGGTTGTATAGGAAAA
1 CATTTTGTTTACTAGTCAAAATTTGGGATATCACAAAGGAAAATATAAAAGGTTGTACAGGAAAA
2083276 AGGGTGGCTACAAGAAAAAATCAAAATGTTAGAATAGAGTAATGGATTAAGATTTTGCAAAAGAA
66 AGGGTGGCTACAAGAAAAAATCAAAATGTTAGAATAGAGTAATGGATTAAGATTTTGCAAAAGAA
2083341 ATAATAGATAGAAATCAAACATTATTGATTTTTTTAAGATGAAGAAAGAATAATCCCCTCACTCT
131 ATAATAGATAGAAATCAAACATTATTGATTTTTTTAAGATGAAGAAAGAATAATCCCCTCACTCT
2083406 TTGAAACTTTTTTTTAATTTATTTTTTTCAAATTTTTTCACAAAATTGGGAGAGGTAAACCTAAA
196 TTGAAACTTTTTTTTAATTTATTTTTTTCAAATTTTTTCACAAAATTGGGAGAGGTAAACCTAAA
* *
2083471 ACTTAATGAATCTTGTAGCTATGCTACCAAATTATATGAATCTGATAGTTTAGTTGTCGAATTTA
261 ACTTAATGAATCTTGTAGCTATGCTACCAAAATATATGAATCTGATAGTGTAGTTGTCGAATTTA
2083536 TATGTGAAATTGCCCGATTATGATTCTAGTAACAGATCAAATGATAACTTTGAATCCTAAAATGA
326 TATGTGAAATTGCCCGATTATGATTCTAGTAACAGATCAAATGATAACTTTGAATCCTAAAATGA
2083601 GATTCATAATGAACCTAACAAAGTGGAAGAGAAGTATATGATT
391 GATTCATAATGAACCTAACAAAGTGGAAGAGAAGTATATGATT
*
2083644 CATTTTGTTTACTAGTCAAAATTTGGGATATCACAGAGGAAAATATAAAAGGTTGTACAGGAAAA
1 CATTTTGTTTACTAGTCAAAATTTGGGATATCACAAAGGAAAATATAAAAGGTTGTACAGGAAAA
2083709 AGGGTGGCTACAAGAAACAAATCAAAATGTTAGAATAGAGTAATGGATTAAGATTTTGCAAAAGA
66 AGGGTGGCTACAAGAAA-AAATCAAAATGTTAGAATAGAGTAATGGATTAAGATTTTGCAAAAGA
2083774 AATAATAGATAGAAATCAAACATTATTGA-TTTTTTAAGATGAAGAAAGAATAATCCCCTCACTC
130 AATAATAGATAGAAATCAAACATTATTGATTTTTTTAAGATGAAGAAAGAATAATCCCCTCACTC
*
2083838 TTTGAAACTTTTTTTTAATTTATTTTTTTCAAATTTTTTCATAAAATTGGGAGAGGTAAACCTAA
195 TTTGAAACTTTTTTTTAATTTATTTTTTTCAAATTTTTTCACAAAATTGGGAGAGGTAAACCTAA
2083903 AACTTAATGAATCTTGTAGCTATGCTACCAAAATATATGAATAC-GATAGTGTAGTTGTCGAATT
260 AACTTAATGAATCTTGTAGCTATGCTACCAAAATATATGAAT-CTGATAGTGTAGTTGTCGAATT
* *
2083967 TATATGTGAAATTGCCCGATTATGATTCTAGTAATAGATCAAATGATAACTTTGAATCCTGAAAT
324 TATATGTGAAATTGCCCGATTATGATTCTAGTAACAGATCAAATGATAACTTTGAATCCTAAAAT
2084032 GAGATTCATAATGAACCTAACAAAGTGGAAGAGAAGTATATG
389 GAGATTCATAATGAACCTAACAAAGTGGAAGAGAAGTATATG
2084074 TTGAAATGCA
Statistics
Matches: 421, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
433 344 0.82
434 77 0.18
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (433 bp):
CATTTTGTTTACTAGTCAAAATTTGGGATATCACAAAGGAAAATATAAAAGGTTGTACAGGAAAA
AGGGTGGCTACAAGAAAAAATCAAAATGTTAGAATAGAGTAATGGATTAAGATTTTGCAAAAGAA
ATAATAGATAGAAATCAAACATTATTGATTTTTTTAAGATGAAGAAAGAATAATCCCCTCACTCT
TTGAAACTTTTTTTTAATTTATTTTTTTCAAATTTTTTCACAAAATTGGGAGAGGTAAACCTAAA
ACTTAATGAATCTTGTAGCTATGCTACCAAAATATATGAATCTGATAGTGTAGTTGTCGAATTTA
TATGTGAAATTGCCCGATTATGATTCTAGTAACAGATCAAATGATAACTTTGAATCCTAAAATGA
GATTCATAATGAACCTAACAAAGTGGAAGAGAAGTATATGATT
Found at i:2085102 original size:18 final size:18
Alignment explanation
Indices: 2085034--2085111 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 18
2085024 ATGCAAACTC
*
2085034 TAAAGGAACTAGTTTAAT
1 TAAATGAACTAGTTTAAT
* *
2085052 T-AATGAACCATTTTAAT
1 TAAATGAACTAGTTTAAT
2085069 TAAATGAACTAGTTTAAT
1 TAAATGAACTAGTTTAAT
2085087 T-AATGAACTAGCTTT-AT
1 TAAATGAACTAG-TTTAAT
*
2085104 TGAATGAA
1 TAAATGAA
2085112 TCATCATACT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
17 27 0.52
18 25 0.48
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (18 bp):
TAAATGAACTAGTTTAAT
Found at i:2085110 original size:35 final size:35
Alignment explanation
Indices: 2085034--2085111 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
2085024 ATGCAAACTC
* *
2085034 TAAAGGAACTAGTTTAATTAATGAACCATTTTAAT
1 TAAATGAACTAGTTTAATTAATGAACCACTTTAAT
*
2085069 TAAATGAACTAGTTTAATTAATGAACTAGCTTT-AT
1 TAAATGAACTAGTTTAATTAATGAACCA-CTTTAAT
*
2085104 TGAATGAA
1 TAAATGAA
2085112 TCATCATACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 35 0.92
36 3 0.08
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (35 bp):
TAAATGAACTAGTTTAATTAATGAACCACTTTAAT
Found at i:2085172 original size:17 final size:17
Alignment explanation
Indices: 2085152--2085194 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
2085142 ATTAAACTAT
2085152 ATGCTTTAATTAACCAC
1 ATGCTTTAATTAACCAC
2085169 ATGCTTTAATTAACCAC
1 ATGCTTTAATTAACCAC
2085186 ATGCTTTAA
1 ATGCTTTAA
2085195 AGGAAGTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (17 bp):
ATGCTTTAATTAACCAC
Found at i:2093493 original size:54 final size:54
Alignment explanation
Indices: 2093433--2093831 Score: 604
Period size: 54 Copynumber: 7.4 Consensus size: 54
2093423 GTTAAGTAGT
** * *
2093433 TTGCACACCCAGTTCCAATACAGAAATTCACAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
* *
2093487 TCGCACACATAGTACCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
* * * *
2093541 TTGCACATATAGTGCCTATACGGAAATTCATAAACTCATTATGGATTTCTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
*
2093595 TTGCACACAAAGTGCCAATAC-GAAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACAG-AAATTCATAAACTCATTATGAATTTCTTAAG
* * *
2093649 TTGCACACATAGTGCCAATACGGAAATTCATAAACCCATTAT-ATATTTTTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGA-ATTTCTTAAG
* * *
2093703 TTGCACACATAGTGTCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
*
2093757 TTGCATACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
2093811 TTGCACACATAGTGCCAATAC
1 TTGCACACATAGTGCCAATAC
2093832 GGTAATCACA
Statistics
Matches: 314, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
53 2 0.01
54 310 0.99
55 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
Found at i:2094302 original size:94 final size:95
Alignment explanation
Indices: 2094167--2094353 Score: 216
Period size: 94 Copynumber: 2.0 Consensus size: 95
2094157 CCATGGTATC
* * * * *
2094167 GATACTTCTATATTGTGGTACCGATACTCCCTTTCAGTATCGATA-CAATTTATACATTCTGG-A
1 GATACTTCTATACTATGGTACCGATACTCCATTACAATATCGATATC-ATTTATACATTCTGGAA
** * **
2094230 TCCTTGGTATCGATATCTTTCTCTTAGTACT
65 TCAATGGTATCGATACCTCCCTCTTAGTACT
** * **
2094261 GATACTTCTATACTATGGTATTGATACTCTATTACAATATCGATATCATTTATGTATTCTGGAAT
1 GATACTTCTATACTATGGTACCGATACTCCATTACAATATCGATATCATTTATACATTCTGGAAT
2094326 CAATGGTATCGATACCTCCCTCTTAGTA
66 CAATGGTATCGATACCTCCCTCTTAGTA
2094354 TCGATACCCA
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
94 50 0.66
95 26 0.34
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (95 bp):
GATACTTCTATACTATGGTACCGATACTCCATTACAATATCGATATCATTTATACATTCTGGAAT
CAATGGTATCGATACCTCCCTCTTAGTACT
Found at i:2095971 original size:18 final size:18
Alignment explanation
Indices: 2095948--2095982 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2095938 GTTCTTAAGG
2095948 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
2095966 AGTGGTCCTTTGGGACA
1 AGTGGTCATTCGGGACA
2095983 AATATACAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:2098615 original size:83 final size:84
Alignment explanation
Indices: 2098433--2098605 Score: 222
Period size: 83 Copynumber: 2.1 Consensus size: 84
2098423 TTCATTTCTT
* * * ** *
2098433 TGAAGGACGCCAAATCGAGGAATGATCTTCCTCCTTCCTCTGAAAGACGCGAAGTCGTAATCGCT
1 TGAAGGATGTCAAATCAAGGAATGATCTTAATCCTCCCTCTGAAAGACGCGAAGTCGTAATCGCT
*
2098498 GGTGATCTACTCCTTCCTC
66 GGTGATCTACTCCTTCATC
* * * * *
2098517 TGAAGGATGTCAAATCAAGGAATGATCTTAATCCTCCCT-TGAAGGATGCTAAGTTGTAATCGGT
1 TGAAGGATGTCAAATCAAGGAATGATCTTAATCCTCCCTCTGAAAGACGCGAAGTCGTAATCGCT
*
2098581 GGTGATCTGCTCCTTCATC
66 GGTGATCTACTCCTTCATC
2098600 TGAAGG
1 TGAAGG
2098606 TCATTAAATC
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
83 43 0.57
84 33 0.43
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (84 bp):
TGAAGGATGTCAAATCAAGGAATGATCTTAATCCTCCCTCTGAAAGACGCGAAGTCGTAATCGCT
GGTGATCTACTCCTTCATC
Found at i:2102122 original size:27 final size:27
Alignment explanation
Indices: 2102091--2102238 Score: 83
Period size: 26 Copynumber: 5.5 Consensus size: 27
2102081 ATTAACCGAA
*
2102091 TATTTTTAACATTAATCGAACCAAAAT
1 TATTTTGAACATTAATCGAACCAAAAT
* * * *
2102118 TA-TTTGACCGTTAATCAAACCCAAAT
1 TATTTTGAACATTAATCGAACCAAAAT
* * *
2102144 T-TATTTGAAAATT-AT-TAACCAAATTT
1 TAT-TTTGAACATTAATCGAACCAAA-AT
* *
2102170 TTTTCTTTAACCATTAATCGAACCAAAAT
1 TATT-TTGAA-CATTAATCGAACCAAAAT
* * *
2102199 TA-TTTGACCGTTAATCGAACCCAAAT
1 TATTTTGAACATTAATCGAACCAAAAT
*
2102225 T-TATTTGAAAATTA
1 TAT-TTTGAACATTA
2102239 TTAACCAAAT
Statistics
Matches: 88, Mismatches: 23, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
25 6 0.07
26 42 0.48
27 25 0.28
28 4 0.05
29 4 0.05
30 7 0.08
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (27 bp):
TATTTTGAACATTAATCGAACCAAAAT
Found at i:2102132 original size:26 final size:26
Alignment explanation
Indices: 2102100--2102232 Score: 108
Period size: 26 Copynumber: 5.0 Consensus size: 26
2102090 ATATTTTTAA
*
2102100 CATTAATCGAACCAAAATTATTTGAC
1 CATTAATCGAACCAAATTTATTTGAC
* * *
2102126 CGTTAATCAAACCCAAATTTATTTGAA
1 CATTAATCGAA-CCAAATTTATTTGAC
* * * *
2102153 AATT-AT-TAACCAAATTTTTTTCTTTAAC
1 CATTAATCGAACCAAA----TTTATTTGAC
*
2102181 CATTAATCGAACCAAAATTATTTGAC
1 CATTAATCGAACCAAATTTATTTGAC
*
2102207 CGTTAATCGAACCCAAATTTATTTGA
1 CATTAATCGAA-CCAAATTTATTTGA
2102233 AAATTATTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
24 5 0.06
25 2 0.02
26 28 0.34
27 28 0.34
28 10 0.12
29 2 0.02
30 7 0.09
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (26 bp):
CATTAATCGAACCAAATTTATTTGAC
Found at i:2102147 original size:90 final size:92
Alignment explanation
Indices: 2101943--2102163 Score: 320
Period size: 90 Copynumber: 2.4 Consensus size: 92
2101933 TCTTTAACCA
* *
2101943 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAATTTTTTTTCTTT
1 TTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAA---TTATTCTTT
* *
2102008 CACATTAATTGAACCAAAATTATTTGACCG
63 AACATTAATCGAACCAAAATTATTTGACCG
* * *
2102038 TTAATCGAATCAAAATTTATTTAAAAATTATTAACCGAACCAAATTAACCGAA-TATT-TTTAAC
1 TTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAATTATTCTTTAAC
2102101 ATTAATCGAACCAAAATTATTTGACCG
66 ATTAATCGAACCAAAATTATTTGACCG
* *
2102128 TTAATCAAACCCAAATTTATTTGAAAATTATTAACC
1 TTAATCGAACCAAAATTTATTTGAAAATTATTAACC
2102164 AAATTTTTTT
Statistics
Matches: 115, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
90 63 0.55
91 3 0.03
95 49 0.43
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (92 bp):
TTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAATTATTCTTTAAC
ATTAATCGAACCAAAATTATTTGACCG
Found at i:2102196 original size:81 final size:80
Alignment explanation
Indices: 2102095--2102249 Score: 292
Period size: 81 Copynumber: 1.9 Consensus size: 80
2102085 ACCGAATATT
2102095 TTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATT
1 TTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATT
2102160 AACCAAATTTTTTTC
66 AACCAAATTTTTTTC
*
2102175 TTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAAATTTATTTGAAAATTAT
1 TTTAA-CATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTAT
2102240 TAACCAAATT
65 TAACCAAATT
2102250 AACCGAATAA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
80 5 0.07
81 68 0.93
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (80 bp):
TTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAAATTTATTTGAAAATTATT
AACCAAATTTTTTTC
Found at i:2102392 original size:94 final size:94
Alignment explanation
Indices: 2102279--2102509 Score: 417
Period size: 94 Copynumber: 2.5 Consensus size: 94
2102269 TTTTTCTTTA
2102279 ACCGTTAATCGAACAGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCC
1 ACCGTTAATCGAACAGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCC
2102344 TTAACCATTAATCGAACCAAAATTATTTG
66 TTAACCATTAATCGAACCAAAATTATTTG
* *
2102373 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCT
1 ACCGTTAATCGAACAGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCC
*
2102438 TTAACCATTAATCGAACCGAAATTATTTG
66 TTAACCATTAATCGAACCAAAATTATTTG
**
2102467 ACCGTTAATCGAATTGAAATTTATTTGAAAATTATTAACCGAA
1 ACCGTTAATCGAACAGAAATTTATTTGAAAATTATTAACCGAA
2102510 TTAACCGAAT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 132 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (94 bp):
ACCGTTAATCGAACAGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCC
TTAACCATTAATCGAACCAAAATTATTTG
Found at i:2102544 original size:38 final size:38
Alignment explanation
Indices: 2102501--2102620 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 38
2102491 TTGAAAATTA
2102501 TTAACCGAATTAACCGAATAGAATAAATTATTTTTTCC
1 TTAACCGAATTAACCGAATAGAATAAATTATTTTTTCC
* ** * * *
2102539 TTAACCG--TTAATCGAACCG-A-AATTTATTTGAAAATT-A
1 TTAACCGAATTAACCGAATAGAATAAATTATTT----TTTCC
**
2102576 TTAACCGAATTAACTAAATAGAATAAATTATTTTTTCC
1 TTAACCGAATTAACCGAATAGAATAAATTATTTTTTCC
2102614 TTAACCG
1 TTAACCG
2102621 TTAATCGAAC
Statistics
Matches: 59, Mismatches: 14, Indels: 18
0.65 0.15 0.20
Matches are distributed among these distances:
34 8 0.14
35 1 0.02
36 9 0.15
37 9 0.15
38 16 0.27
39 7 0.12
40 1 0.02
41 8 0.14
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (38 bp):
TTAACCGAATTAACCGAATAGAATAAATTATTTTTTCC
Found at i:2102596 original size:75 final size:75
Alignment explanation
Indices: 2102467--2102661 Score: 345
Period size: 75 Copynumber: 2.6 Consensus size: 75
2102457 AAATTATTTG
** *
2102467 ACCGTTAATCGAATTGAAATTTATTTGAAAATTATTAACCGAATTAACCGAATAGAATAAATTAT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAATTAACCAAATAGAATAAATTAT
2102532 TTTTTCCTTA
66 TTTTTCCTTA
*
2102542 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAATTAACTAAATAGAATAAATTAT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAATTAACCAAATAGAATAAATTAT
2102607 TTTTTCCTTA
66 TTTTTCCTTA
*
2102617 ACCGTTAATCGAACCGAAATGTATTTGAAAATTATTAACCGAATT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAATT
2102662 TTTTCTTTAA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 115 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (75 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAATTAACCAAATAGAATAAATTAT
TTTTTCCTTA
Found at i:2102697 original size:27 final size:27
Alignment explanation
Indices: 2102614--2102698 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
2102604 TATTTTTTCC
* *
2102614 TTAACCGTTAATCGAACCGAAATGTAT
1 TTAACCATTAATCGAACCGAAATTTAT
* * * *
2102641 TTGAA-AATT-AT-TAACCGAATTTTTTCT
1 TT-AACCATTAATCGAACCGAA--ATTTAT
2102668 TTAACCATTAATCGAACCGAAATTTAT
1 TTAACCATTAATCGAACCGAAATTTAT
2102695 TTAA
1 TTAA
2102699 ACAAATAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
25 7 0.17
26 4 0.10
27 20 0.48
28 4 0.10
29 7 0.17
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (27 bp):
TTAACCATTAATCGAACCGAAATTTAT
Found at i:2105617 original size:20 final size:18
Alignment explanation
Indices: 2105589--2105639 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
2105579 GATTAGAACA
*
2105589 AAATAAAAAAAAAGATAAAG
1 AAATTAAAAAAAA-AT-AAG
2105609 AAATTAAAAATAAAATAAG
1 AAATTAAAAA-AAAATAAG
2105628 ATAA-TAAAAAAA
1 A-AATTAAAAAAA
2105640 CCAAAAGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 13 0.46
21 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (18 bp):
AAATTAAAAAAAAATAAG
Found at i:2108935 original size:175 final size:178
Alignment explanation
Indices: 2108644--2108996 Score: 685
Period size: 175 Copynumber: 2.0 Consensus size: 178
2108634 ATAATGTTTT
2108644 AGATAATGAAAAAGAACAATAAAAAGGAAAAACAAATGAACCTAAAGCACTAAGAGTCAAAGAAA
1 AGATAATGAAAAAGAACAATAAAAAGGAAAAACAAATGAACCTAAAGCACTAAGAGTCAAAGAAA
2108709 AAAAAAAGAACCAAACCAGAAACATAGAAAACGTTGGGTCAACTTGAGAAACA-TTTTGAGCGGT
66 AAAAAAAGAACCAAACCAGAAACATAGAAAACGTTGGGTCAACTTGAGAAACATTTTTGAGCGGT
2108773 TTACCGGTGTC-AAAAATTCTGTAAAAAATCTTG-ATGTCTTTCGATG
131 TTACCGGTGTCAAAAAATTCTGTAAAAAATCTTGAATGTCTTTCGATG
2108819 AGATAATGAAAAAGAACAATAAAAAGGAAAAACAAATGAACCTAAAGCACTAAGAGTCAAAGAAA
1 AGATAATGAAAAAGAACAATAAAAAGGAAAAACAAATGAACCTAAAGCACTAAGAGTCAAAGAAA
2108884 AAAAAAAGAACCAAACCAGAAACATAGAAAACGTTGGGTCAACTTGAGAAACATTTTTGAGCGGT
66 AAAAAAAGAACCAAACCAGAAACATAGAAAACGTTGGGTCAACTTGAGAAACATTTTTGAGCGGT
2108949 TTACCGGTGTCAAAAAATTCTGTAAAAAATCTTGAATGTCTTTCGATG
131 TTACCGGTGTCAAAAAATTCTGTAAAAAATCTTGAATGTCTTTCGATG
2108997 CATGGAGAAA
Statistics
Matches: 175, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
175 118 0.67
176 22 0.13
177 22 0.13
178 13 0.07
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.20
Consensus pattern (178 bp):
AGATAATGAAAAAGAACAATAAAAAGGAAAAACAAATGAACCTAAAGCACTAAGAGTCAAAGAAA
AAAAAAAGAACCAAACCAGAAACATAGAAAACGTTGGGTCAACTTGAGAAACATTTTTGAGCGGT
TTACCGGTGTCAAAAAATTCTGTAAAAAATCTTGAATGTCTTTCGATG
Found at i:2113199 original size:14 final size:14
Alignment explanation
Indices: 2113174--2113273 Score: 127
Period size: 14 Copynumber: 7.3 Consensus size: 14
2113164 AATGTTGTTC
* *
2113174 AAACTCTTAACCTT
1 AAACTCTAAACCCT
*
2113188 AAAC-CTTAAACCTT
1 AAACTC-TAAACCCT
2113202 AAACTCTAAACCCT
1 AAACTCTAAACCCT
2113216 AAACTCTAAACCCT
1 AAACTCTAAACCCT
2113230 AAACTCTAAACCCT
1 AAACTCTAAACCCT
2113244 AAACTCT--ACCCT
1 AAACTCTAAACCCT
2113256 AAA-TCTTAAACCCT
1 AAACTC-TAAACCCT
2113270 AAAC
1 AAAC
2113274 CCTATCACAT
Statistics
Matches: 78, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
11 2 0.03
12 9 0.12
13 1 0.01
14 65 0.83
15 1 0.01
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACTCTAAACCCT
Found at i:2113272 original size:7 final size:7
Alignment explanation
Indices: 2113182--2113277 Score: 97
Period size: 7 Copynumber: 14.0 Consensus size: 7
2113172 TCAAACTCTT
*
2113182 AACCTTA
1 AACCCTA
*
2113189 AACCTTA
1 AACCCTA
*
2113196 AACCTTA
1 AACCCTA
*
2113203 AACTCTA
1 AACCCTA
2113210 AACCCTA
1 AACCCTA
*
2113217 AACTCTA
1 AACCCTA
2113224 AACCCTA
1 AACCCTA
*
2113231 AACTCTA
1 AACCCTA
2113238 AACCCTA
1 AACCCTA
*
2113245 AACTCT-
1 AACCCTA
2113251 -ACCCTA
1 AACCCTA
* *
2113257 AATCTTA
1 AACCCTA
2113264 AACCCTA
1 AACCCTA
2113271 AACCCTA
1 AACCCTA
2113278 TCACATAATT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
5 4 0.05
7 70 0.95
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (7 bp):
AACCCTA
Found at i:2121716 original size:12 final size:12
Alignment explanation
Indices: 2121694--2121733 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2121684 TATAAATTAT
2121694 AATTATAAGTTTA
1 AATT-TAAGTTTA
*
2121707 AGTTTAAGTTTA
1 AATTTAAGTTTA
*
2121719 AATTTAAATTTA
1 AATTTAAGTTTA
2121731 AAT
1 AAT
2121734 AATATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
AATTTAAGTTTA
Found at i:2129131 original size:13 final size:13
Alignment explanation
Indices: 2129113--2129142 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2129103 GAGATGAAAG
2129113 AAAGTAAAAGTGA
1 AAAGTAAAAGTGA
2129126 AAAGTAAAAGTGA
1 AAAGTAAAAGTGA
2129139 AAAG
1 AAAG
2129143 AAGATAAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.13
Consensus pattern (13 bp):
AAAGTAAAAGTGA
Found at i:2142251 original size:18 final size:16
Alignment explanation
Indices: 2142216--2142255 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
2142206 TTGTTGTTTG
2142216 TTCTTTCAACTTCTTT
1 TTCTTTCAACTTCTTT
*
2142232 TTCTTTGCAATTTCCTTT
1 TTCTTT-CAACTT-CTTT
2142250 TTCTTT
1 TTCTTT
2142256 TCCCTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 5 0.24
18 10 0.48
ACGTcount: A:0.10, C:0.23, G:0.03, T:0.65
Consensus pattern (16 bp):
TTCTTTCAACTTCTTT
Found at i:2155885 original size:7 final size:7
Alignment explanation
Indices: 2155873--2155902 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2155863 TTTTACATCA
2155873 TATTCTT
1 TATTCTT
*
2155880 TATTCTA
1 TATTCTT
2155887 TATTCTT
1 TATTCTT
2155894 TATTCTT
1 TATTCTT
2155901 TA
1 TA
2155903 CATTCCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTCTT
Found at i:2158709 original size:20 final size:20
Alignment explanation
Indices: 2158681--2158760 Score: 88
Period size: 20 Copynumber: 3.7 Consensus size: 20
2158671 TTCATTTATG
*
2158681 GCATTCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
2158701 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
2158726 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
2158747 GCATCCTTTCATGC
1 GCATCCTTTCATGC
2158761 ATTTCATTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
20 27 0.53
21 4 0.08
22 1 0.02
24 1 0.02
25 4 0.08
26 14 0.27
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:2158721 original size:46 final size:46
Alignment explanation
Indices: 2158669--2158774 Score: 203
Period size: 46 Copynumber: 2.3 Consensus size: 46
2158659 TTAATCATTA
*
2158669 ATTTCATTTATGGCATTCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
2158715 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
2158761 ATTTCATTTATGGC
1 ATTTCATTTATGGC
2158775 TTCGTTTTAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:2159496 original size:11 final size:11
Alignment explanation
Indices: 2159468--2159498 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2159458 TTTCATCTTG
*
2159468 ATTTTCACTAA
1 ATTTTCCCTAA
2159479 ATTTTCCCTAA
1 ATTTTCCCTAA
2159490 ATTTTCCCT
1 ATTTTCCCT
2159499 TTTAATCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTTCCCTAA
Found at i:2165447 original size:20 final size:20
Alignment explanation
Indices: 2165421--2165591 Score: 90
Period size: 20 Copynumber: 7.7 Consensus size: 20
2165411 TCATTTATGA
2165421 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
2165441 TATCCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
*
2165467 CATCCTTTCATGCCTAAATG
1 CATCCTTTCATGCCTTAATG
*
2165487 CATCCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
*
2165513 CATCCTTTCATGCCTCAATG
1 CATCCTTTCATGCCTTAATG
* *
2165533 CATCCTTTCGTGCACTTCATTTGTGG
1 CATCCTTTCATGC-CTT-A---AT-G
* *
2165559 AATCTTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
2165579 CATCATTTCATGC
1 CATCCTTTCATGC
2165592 ATTTCATTTA
Statistics
Matches: 115, Mismatches: 18, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
20 51 0.44
21 9 0.08
22 3 0.03
24 3 0.03
25 11 0.10
26 38 0.33
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:2165459 original size:46 final size:46
Alignment explanation
Indices: 2165408--2165617 Score: 330
Period size: 46 Copynumber: 4.6 Consensus size: 46
2165398 TTAATCATTA
* *
2165408 ATTTCATTTATGACATCCTTTCATGCCTTAATGTATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
2165454 ATTTCATTTATGGCATCCTTTCATGCCTAAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
2165500 ATTTCATTTATGGCATCCTTTCATGCCTCAATGCATCCTTTCGTGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * * *
2165546 ACTTCATTTGTGGAATCTTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
2165592 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
2165618 TCATATTGGC
Statistics
Matches: 148, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 148 1.00
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.43
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:2166510 original size:6 final size:5
Alignment explanation
Indices: 2166495--2166592 Score: 101
Period size: 5 Copynumber: 18.6 Consensus size: 5
2166485 TATGCTTAAG
*
2166495 AAAGA AAAGAA AAAGA AAAGAA AAAGA AAAGA AAAGA AAA-A AGA-A AAAGAA
1 AAAGA AAAG-A AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAAG-A
*
2166546 AAAGGA AAGGA AAAGGA AAAGGA AAAGGA AAAGA AAAGA AAAGA AAA
1 AAA-GA AAAGA AAA-GA AAA-GA AAA-GA AAAGA AAAGA AAAGA AAA
2166593 TGAGGGTTCA
Statistics
Matches: 83, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
4 6 0.07
5 42 0.51
6 34 0.41
7 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:2166511 original size:11 final size:11
Alignment explanation
Indices: 2166495--2166592 Score: 117
Period size: 11 Copynumber: 8.7 Consensus size: 11
2166485 TATGCTTAAG
2166495 AAAGAAAAGAA
1 AAAGAAAAGAA
2166506 AAAGAAAAGAA
1 AAAGAAAAGAA
2166517 AAAGAAAAGAA
1 AAAGAAAAGAA
*
2166528 AAGAAAAAAGAA
1 AA-AGAAAAGAA
*
2166540 AAAGAAAAAGGA
1 AAAG-AAAAGAA
*
2166552 AAGGAAAAGGAA
1 AAAGAAAA-GAA
* *
2166564 AAGGAAAAGGA
1 AAAGAAAAGAA
2166575 AAAGAAAAG-A
1 AAAGAAAAGAA
2166585 AAAGAAAA
1 AAAGAAAA
2166593 TGAGGGTTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.12
11 39 0.51
12 29 0.38
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:2167737 original size:135 final size:134
Alignment explanation
Indices: 2167494--2168297 Score: 682
Period size: 135 Copynumber: 6.1 Consensus size: 134
2167484 AGATAAACTA
* * * *
2167494 ATTAACATTTCCAATGGAGAGTT-GTAATGAAAAGAACTCACCCGATAG-AGGAAGAAGAAGTTA
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGG-AGAAGAAGTTC
* * * * * * *
2167557 GTAATGAAAAAAACTTTTTCAAACTTTGTTTGATTCATGGCATTTTGAATCAACGAAACCTCACT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCA-GGCATTTCGAATCAACGAAACCTCACT
2167622 TAAGGG
129 TAAGGG
* * * * * *
2167628 ATTAACTTTTCCAATGTAGAGTTCGTAATGAGAATAAATCATCTGA-ATGAAGGAGAAGAAGTTC
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATA-GAAGGAGAAGAAGTTC
* * ** * *
2167692 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAGTATTTTAAATCAGCGAAACCTTACT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCA-GGCATTTCGAATCAACGAAACCTCACT
*
2167757 TGAGGG
129 TAAGGG
* * * * * *
2167763 ATTAACATTTTCAATGGAGAGTT-ATAAT---TAGAACTCATCCGATAGAGGGCGAATAAGTTGG
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCG
* * * * * * * * *
2167824 TAATTAGAAGAACTTGTTCAACCTTTTCTCTATTCACGGTATTTTGAATTAGCAAAACCTCAATT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCA-GGCATTTCGAATCAACGAAACCTCACTT
2167889 AAGGG
130 AAGGG
** * * * *
2167894 ATTAACATTTATAATGGAGAGTTCGTAATGAGAAGAACTCACCCGATATAAGGAGAAAAAGTTC-
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCG
* * * * *
2167958 --AT------AA-----TCAACCTTTGCTCGATTCATGACATTTCAAATCAGCAAAAGCTCACTT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCA-GGCATTTCGAATCAACGAAACCTCACTT
*
2168010 GAGGG
130 AAGGG
* * *
2168015 ATTAACATTTCCAATGGAGAGTTCACAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCG
** * * * * *
2168080 TGTTGAGAAGAACTTGTTTAACCTTTTCTCGATTAATGACATTTCGAATC-ACCAACACCTCA-T
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCA-GGCATTTCGAATCAACGAA-ACCTCACT
***
2168143 TGAAATA
129 T-AAGGG
* * * * * * *
2168150 ATTAATATTTCCAATGGAGACTTTATAATGAGAATAACTCATCCAATAGAGGGATAAGAAGTTCG
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCG
* * * *
2168215 TAATGAGAATAACTTGTTCAACCTTTGCTCAATTCATGGCATTTCGAATCAACGATACCTTACTT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCA-GGCATTTCGAATCAACGAAACCTCACTT
2168280 AAGGG
130 AAGGG
2168285 ATTAACATTTCCA
1 ATTAACATTTCCA
2168298 GCAAACTGCT
Statistics
Matches: 537, Mismatches: 107, Indels: 51
0.77 0.15 0.07
Matches are distributed among these distances:
121 98 0.18
124 1 0.00
126 2 0.00
130 2 0.00
131 104 0.19
132 7 0.01
134 31 0.06
135 284 0.53
136 8 0.01
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (134 bp):
ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCG
TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCAGGCATTTCGAATCAACGAAACCTCACTTA
AGGG
Found at i:2168181 original size:256 final size:252
Alignment explanation
Indices: 2167710--2168190 Score: 572
Period size: 256 Copynumber: 1.9 Consensus size: 252
2167700 AAGAACTTGT
* * * * *
2167710 TCAACCTTTGCTCGATTCACAGTATTTTAAATCAGCGAAACCTTACTTGAGGGATTAACATTTTC
1 TCAACCTTTGCTCGATTCACAGCATTTCAAATCAGCAAAACCTCACTTGAGGGATTAACATTTCC
* * * * **
2167775 AATGGAGAGTTATAATTAGAACTCATCCGATAGAGGGCGAATAAGTTGGTAATTAGAAGAACTTG
66 AATGGAGAGTTACAATAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATTAGAAGAACTTG
* * ** * * * * *
2167840 TTCAACCTTTTCTCTATTCACGGTATTTTGAATTAGCAAAACCTCAATTAAGGGATTAACATTTA
131 TTCAACCTTTTCTCGATTAACGACATTTCGAATCACCAAAACCTCAATTAAAGAATTAACATTTA
* * *
2167905 TAATGGAGAGTTCGTAATGAGAAGAACTCACCCGATATAAGGAGAAAAAGTTCATAA
196 CAATGGAGACTTCATAATGAGAAGAACTCACCCGATATAAGGAGAAAAAGTTCATAA
* *
2167962 TCAACCTTTGCTCGATTCA-TGACATTTCAAATCAGCAAAAGCTCACTTGAGGGATTAACATTTC
1 TCAACCTTTGCTCGATTCACAG-CATTTCAAATCAGCAAAACCTCACTTGAGGGATTAACATTTC
*
2168026 CAATGGAGAGTTCACAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCAT-GTTGAGAAG
65 CAATGGAGAGTT-ACAAT---AAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATT-AGAAG
* * * *
2168090 AACTTGTTTAACCTTTTCTCGATTAATGACATTTCGAATCACCAACACCTC-ATTGAAATAATTA
125 AACTTGTTCAACCTTTTCTCGATTAACGACATTTCGAATCACCAAAACCTCAATT-AAAGAATTA
* * * *
2168154 ATATTTCCAATGGAGACTTTATAATGAGAATAACTCA
189 ACATTTACAATGGAGACTTCATAATGAGAAGAACTCA
2168191 TCCAATAGAG
Statistics
Matches: 188, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
251 1 0.01
252 67 0.36
253 4 0.02
255 5 0.03
256 111 0.59
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (252 bp):
TCAACCTTTGCTCGATTCACAGCATTTCAAATCAGCAAAACCTCACTTGAGGGATTAACATTTCC
AATGGAGAGTTACAATAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATTAGAAGAACTTG
TTCAACCTTTTCTCGATTAACGACATTTCGAATCACCAAAACCTCAATTAAAGAATTAACATTTA
CAATGGAGACTTCATAATGAGAAGAACTCACCCGATATAAGGAGAAAAAGTTCATAA
Found at i:2172032 original size:19 final size:19
Alignment explanation
Indices: 2172008--2172045 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2171998 GAAGAAAGAC
2172008 AAAATATTAGTAAGTAGAT
1 AAAATATTAGTAAGTAGAT
2172027 AAAATATTAGTAAGTAGAT
1 AAAATATTAGTAAGTAGAT
2172046 GTATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (19 bp):
AAAATATTAGTAAGTAGAT
Found at i:2173781 original size:18 final size:17
Alignment explanation
Indices: 2173753--2173803 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
2173743 TTTTATTTTA
2173753 ATTTA-ATTAATATAAAT
1 ATTTATATTAAT-TAAAT
2173770 ATTTATATTAATTAAAT
1 ATTTATATTAATTAAAT
2173787 ATGTTATAATTAATTAA
1 AT-TTAT-ATTAATTAA
2173804 TTTAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
ATTTATATTAATTAAAT
Found at i:2173800 original size:19 final size:18
Alignment explanation
Indices: 2173756--2173803 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
2173746 TATTTTAATT
2173756 TAATTAATATAAATATTTA
1 TAATTAAT-TAAATATTTA
2173775 T-ATTAATTAAATATGTTA
1 TAATTAATTAAATAT-TTA
2173793 TAATTAATTAA
1 TAATTAATTAA
2173804 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.26
18 10 0.37
19 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATTAATTAAATATTTA
Found at i:2178587 original size:19 final size:19
Alignment explanation
Indices: 2178547--2178587 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2178537 TTTTCTCTTC
*
2178547 ATATTTAAAAAAAATAGCT
1 ATATTTAAAAAAAATAGAT
2178566 ATATTTAAAACAAAATA-AT
1 ATATTTAAAA-AAAATAGAT
2178585 ATA
1 ATA
2178588 CTACTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATTTAAAAAAAATAGAT
Found at i:2181609 original size:27 final size:27
Alignment explanation
Indices: 2181573--2181651 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
2181563 TAACTATATA
2181573 TATATATATATAAACTATATA-TATAGT
1 TATATATATATAAACTATATAGTATA-T
2181600 TATATATATATAAACTATATAGT-TCAT
1 TATATATATATAAACTATATAGTAT-AT
*
2181627 TA-GTATATATAAACTATATAGTATA
1 TATATATATATAAACTATATAGTATA
2181652 CCTAAATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
26 20 0.42
27 26 0.54
28 2 0.04
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (27 bp):
TATATATATATAAACTATATAGTATAT
Found at i:2181620 original size:2 final size:2
Alignment explanation
Indices: 2181446--2181611 Score: 140
Period size: 2 Copynumber: 86.0 Consensus size: 2
2181436 TTAAATAAAT
*
2181446 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2181487 TA TA TA TA TT TA -A TA TA -A T- TT TA TA -A TA TA TA GT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
2181525 TA TA -A CTA TA T- TA TA TA T- TA -A TA AA TA TA GTT TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
2181565 -A CTA TA TA TA TA TA TA TA TA AA CTA TA TA TA TA GT- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA
2181606 TA TA TA
1 TA TA TA
2181612 AACTATATAG
Statistics
Matches: 135, Mismatches: 11, Indels: 36
0.74 0.06 0.20
Matches are distributed among these distances:
1 12 0.09
2 117 0.87
3 6 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2181660 original size:24 final size:26
Alignment explanation
Indices: 2181592--2181648 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
2181582 ATAAACTATA
*
2181592 TATATAGTT-A-TA-TATATATAAAC
1 TATATAGTTCATTACTAAATATAAAC
* *
2181615 TATATAGTTCATTAGTATATATAAAC
1 TATATAGTTCATTACTAAATATAAAC
2181641 TATATAGT
1 TATATAGT
2181649 ATACCTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 9 0.29
24 1 0.03
25 2 0.06
26 19 0.61
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (26 bp):
TATATAGTTCATTACTAAATATAAAC
Found at i:2181660 original size:26 final size:27
Alignment explanation
Indices: 2181578--2181660 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
2181568 ATATATATAT
* *
2181578 ATATATAAACTATATA-TATAGTTATA
1 ATATATAAACTATATAGTATACTTAGA
*
2181604 TATATATAAACTATATAGT-T-CATTAGT
1 -ATATATAAACTATATAGTATAC-TTAGA
*
2181631 ATATATAAACTATATAGTATACCTA-A
1 ATATATAAACTATATAGTATACTTAGA
2181657 ATAT
1 ATAT
2181661 TTTGTTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 22 0.47
27 23 0.49
28 2 0.04
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (27 bp):
ATATATAAACTATATAGTATACTTAGA
Found at i:2182356 original size:26 final size:26
Alignment explanation
Indices: 2182326--2182377 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2182316 TATAAAAAGT
2182326 AAACATGTAATAATATTTAATTTTTA
1 AAACATGTAATAATATTTAATTTTTA
2182352 AAACATGTAATAATATTTAATTTTTA
1 AAACATGTAATAATATTTAATTTTTA
2182378 GCTTAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
AAACATGTAATAATATTTAATTTTTA
Found at i:2182859 original size:20 final size:20
Alignment explanation
Indices: 2182813--2182867 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
2182803 TAATAAGTCT
* * *
2182813 ATTTATTAATTTAATTATCAT
1 ATTTAATAA-TTAATTATAAC
*
2182834 AATTAATAATTAATTATAAC
1 ATTTAATAATTAATTATAAC
*
2182854 ATTTAAAAATTAAT
1 ATTTAATAATTAAT
2182868 CATATTAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAATAATTAATTATAAC
Found at i:2186852 original size:3 final size:3
Alignment explanation
Indices: 2186844--2186884 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
2186834 CACATATGTT
2186844 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T
2186885 ACCTTAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2186868 original size:22 final size:22
Alignment explanation
Indices: 2186843--2186884 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2186833 ACACATATGT
2186843 TTTATTATTATTATTATTATTA
1 TTTATTATTATTATTATTATTA
2186865 TTTATTATTATTATTATTAT
1 TTTATTATTATTATTATTAT
2186885 ACCTTAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTATTATTATTATTATTA
Found at i:2186871 original size:19 final size:19
Alignment explanation
Indices: 2186847--2186884 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2186837 ATATGTTTTA
2186847 TTATTATTATTATTATTAT
1 TTATTATTATTATTATTAT
2186866 TTATTATTATTATTATTAT
1 TTATTATTATTATTATTAT
2186885 ACCTTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTATTATTATTAT
Done.